1WDW

Structural basis of mutual activation of the tryptophan synthase a2b2 complex from a hyperthermophile, Pyrococcus furiosus

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

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This is version 1.2 of the entry. See complete history. 


Literature

Conformational Changes in the Tryptophan Synthase from a Hyperthermophile upon alpha(2)beta(2) Complex Formation: Crystal Structure of the Complex

Lee, S.J., Ogasahara, K., Ma, J., Nishio, K., Ishida, M., Yamagata, Y., Tsukihara, T., Yutani, K.

(2005) Biochemistry 44: 11417-11427

  • DOI: 10.1021/bi050317h
  • Primary Citation of Related Structures:  
    1WDW

  • PubMed Abstract: 

    • The three-dimensional structure of the bifunctional tryptophan synthase alpha(2)beta(2) complex from Pyrococcus furiosus was determined by crystallographic analysis. This crystal structure, with the structures of an alpha subunit monomer and a beta(2) subunit dimer that have already been reported, is the first structural set in which changes in structure that occur upon the association of the individual tryptophan synthase subunits were observed ...

    The three-dimensional structure of the bifunctional tryptophan synthase alpha(2)beta(2) complex from Pyrococcus furiosus was determined by crystallographic analysis. This crystal structure, with the structures of an alpha subunit monomer and a beta(2) subunit dimer that have already been reported, is the first structural set in which changes in structure that occur upon the association of the individual tryptophan synthase subunits were observed. To elucidate the structural basis of the stimulation of the enzymatic activity of each of the alpha and beta(2) subunits upon alpha(2)beta(2) complex formation, the conformational changes due to complex formation were analyzed in detail compared with the structures of the alpha monomer and beta(2) subunit dimer. The major conformational changes due to complex formation occurred in the region correlated with the catalytic function of the enzyme as follows. (1) Structural changes in the beta subunit were greater than those in the alpha subunit. (2) Large movements of A46 and L165 in the alpha subunit due to complex formation caused a more open conformation favoring the entry of the substrate at the alpha active site. (3) The major changes in the beta subunit were the broadening of a long tunnel through which the alpha subunit product (indole) is transferred to the beta active site and the opening of an entrance at the beta active site. (4) The changes in the conformations of both the alpha and beta subunits due to complex formation contributed to the stabilization of the subunit association, which is critical for the stimulation of the enzymatic activities.

    Organizational Affiliation: 

    Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tryptophan synthase alpha chain
A, C, E, G, I, K
A, C, E, G, I, K
248Pyrococcus furiosusMutation(s): 0 
Gene Names: trpA
EC: 4.2.1.20
UniProt
Find proteins for Q8U094 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U094 
Go to UniProtKB:  Q8U094
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8U094
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tryptophan synthase beta chain 1
B, D, F, H, J, L
B, D, F, H, J, L
385Pyrococcus furiosusMutation(s): 0 
Gene Names: TRPB
EC: 4.2.1.20
UniProt
Find proteins for Q8U093 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore Q8U093 
Go to UniProtKB:  Q8U093
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8U093
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP
Download Ideal Coordinates CCD File 
M [auth B],
N [auth D],
O [auth F],
P [auth H],
Q [auth J],
M [auth B],
N [auth D],
O [auth F],
P [auth H],
Q [auth J],
R [auth L]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.056α = 90
b = 220.257β = 90
c = 292.56γ = 90
Software Package:
Software NamePurpose
CNSrefinement
d*TREKdata scaling
EPMRphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-07-12
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance